Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Astro"
graph_weight
## [1] "1.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   39.00   41.00   43.00   42.52   44.00   45.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 39 40 41 41 41 41 41 41 41 41 41 41 42 42 42 42 42 42 43 43 43 43 43 43 43
## [26] 43 43 43 43 44 44 44 44 44 44 44 44 45 45 45

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1643   357
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    21  1622   357
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:       BTBD11       ABTB3
##  2:    LINC01006    RNF32-DT
##  3:    LINC01185      REL-DT
##  4:   ZRANB2-AS2   ZRANB2-DT
##  5:    LINC00271     AHI1-DT
##  6:     RFX3-AS1     RFX3-DT
##  7:    COX10-AS1    COX10-DT
##  8:   SUCLG2-AS1   SUCLG2-DT
##  9:      C5orf17   LINC02899
## 10:     OSMR-AS1     OSMR-DT
## 11:  C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2   TENM2-AS1
## 13:    LINC00637 PPP1R13B-DT
## 14:         MPP6    MPHOSPH6
## 15:      C7orf61      SPACDR
## 16:      C3orf35       APRG1
## 17:       HRAT92    PDGFA-DT
## 18:    LINC00884  ATP13A3-DT
## 19:    LINC01137  ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21:      MAFG-DT       MILIP
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
## 3:        ASB4      ASB4        ASB4
## 4:       USH1C     USH1C       USH1C
## 5:    ARHGAP44  ARHGAP44    ARHGAP44
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1 
## 2000

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:        CD38      CD38        CD38
## 2:     PRKAR2B   PRKAR2B     PRKAR2B
gene_dat = fread(sprintf("data/%s_genes_info.csv", cell_type_name))
dim(gene_dat)
## [1] 36517     9
gene_dat[1:2,]
##           gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003               FALSE       TSPAN6    NCBITaxon:9606
## 2: ENSG00000000005               FALSE         TNMD    NCBITaxon:9606
##    feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1:            gene              6900 0.118699020              90.14412
## 2:            gene               161 0.002485395              99.77003
##    total_counts
## 1:         8310
## 2:          174
length(unique(gene_info$sym_in_data))
## [1] 2000
table(gene_info$sym_in_data %in% gene_dat$feature_name)
## 
## TRUE 
## 2000
table(gene_dat$feature_name %in% gene_info$sym_in_data)
## 
## FALSE  TRUE 
## 34517  2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1

table(gene_dat$selected)
## 
##     0     1 
## 34517  2000
tapply(gene_dat$pct_dropout_by_counts, gene_dat$selected, summary)
## $`0`
##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
##   0.00857  90.44551  99.20296  90.72478  99.93429 100.00000 
## 
## $`1`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00   60.04   81.87   72.81   92.88   97.99
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data", 
                  by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)
## [1] 2000   12
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol        gene_ids feature_is_filtered
## 1:         A2M       A2M         A2M ENSG00000175899               FALSE
## 2:   A2ML1-AS1 A2ML1-AS1   A2ML1-AS1 ENSG00000256661               FALSE
##    feature_reference feature_biotype n_cells_by_counts mean_counts
## 1:    NCBITaxon:9606            gene              5826   0.1207987
## 2:    NCBITaxon:9606            gene             11030   0.2138297
##    pct_dropout_by_counts total_counts selected
## 1:              91.67821         8457        1
## 2:              84.24488        14970        1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol", 
              bias.data = 100 - gene_info$pct_dropout_by_counts)
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "MYO16"    "PPEF1"    "EPB41L4B" "SCD"      "GALNT16"  "FRK"     
##  [7] "SIPA1L2"  "APOC1"    "EPSTI1"   "C4orf45"  "EPHX4"    "SSR4"    
## [13] "ARHGAP8"  "CCDC124"  "DCN"      "ABCA7"    "ATP2B3"   "PPP1R15A"
## [19] "CASS4"    "SLC7A5"   "RELB"     "ISYNA1"   "ADAP1"    "EPHB6"   
## [25] "UNC5B"    "ARID3A"   "DUSP1"    "PMEPA1"   "ANXA1"    "HAVCR2"  
## [31] "MICAL1"   "MVB12A"   "SH3GL1"   "SLC43A1"  "CNKSR3"   "FBXO32"  
## [37] "PDPN"     "ITGA2"    "PIK3CD"   "MYO1D"    "MB21D2"   "TMEM229B"
## [43] "HAUS7"

## [1] 2
##  [1] "AHRR"          "SLC26A8"       "WDR64"         "FILIP1L"      
##  [5] "GLIPR1L1"      "AP000233.4"    "RP1-15D23.2"   "TMLHE-AS1"    
##  [9] "RP11-547I7.1"  "ST7-AS2"       "AC017101.10"   "ASTN2-AS1"    
## [13] "CCDC192"       "RP11-417B4.2"  "RP11-46O21.2"  "GRM3-AS1"     
## [17] "AC037445.1"    "RP11-666F17.1" "RP11-109I13.2" "LINC02250"    
## [21] "LINC01695"     "LINC01829"     "GS1-433O24.1"  "AC008067.2"   
## [25] "LINC02877"     "RP11-657O9.1"  "RP5-1101C3.1"  "GK-AS1"       
## [29] "RP11-115N4.1"  "RP11-274H2.2"  "RP11-223C24.1" "RP11-120A1.1" 
## [33] "RP11-39E3.3"   "CTD-3239E11.2" "RP11-463D19.1" "RP11-1H15.2"  
## [37] "A2ML1-AS1"     "RP11-887P2.5"  "DIO2-AS1"      "CRIM1-DT"     
## [41] "RP11-58G13.1"  "CH17-140K24.2" "RP11-313M3.2"  "RP11-394G3.3" 
## [45] "RP11-555K12.4"

## [1] 3
##  [1] "SEL1L2"        "POLR2I"        "H3-3B"         "CA1"          
##  [5] "AGBL3"         "MEGF11"        "BTG2"          "SHOC1"        
##  [9] "MFSD4B"        "SGCZ"          "MT1X"          "HES4"         
## [13] "RP1-292B18.4"  "RP11-131L23.1" "MRPS9-AS2"     "SNAP25-AS1"   
## [17] "GNA14-AS1"     "RP1-232L24.3"  "AC009501.4"    "GNG12-AS1"    
## [21] "LINC00513"     "RBMS3-AS3"     "ZBTB20-AS5"    "PRKAR2B-AS1"  
## [25] "RORA-AS1"      "LINC01618"     "RP11-157I4.4"  "RP11-452H21.1"
## [29] "MPPED2-AS1"    "AP000487.6"    "CTD-2537O9.1"  "LINC02740"    
## [33] "LINC02745"     "RP11-144F15.1" "LINC02327"     "RP11-363J20.2"
## [37] "RP11-524F11.2" "CTC-513N18.6"  "ARRDC3-AS1"    "RP11-470M1.2" 
## [41] "BCL6-AS1"      "CTD-2313D3.2"  "RP11-592G13.2" "RP11-341N18.1"

## [1] 4
##  [1] "WSCD2"         "SRPX2"         "TENT5A"        "DNAH6"        
##  [5] "PKIB"          "HS3ST3A1"      "SAXO1"         "SCN11A"       
##  [9] "FSTL5"         "RNF212"        "CLDN4"         "RFX8"         
## [13] "NPSR1-AS1"     "COL5A2"        "MT1H"          "RP11-306O13.1"
## [17] "AC007277.3"    "RNF212B"       "RP11-344B5.2"  "RP11-735G4.1" 
## [21] "LINC01036"     "AC009264.1"    "LINC01934"     "LINC01376"    
## [25] "RP11-624M8.1"  "PTPRG-AS1"     "RP11-167H9.4"  "LINC02355"    
## [29] "RP11-436F23.1" "ZFHX4-AS1"     "C8orf37-AS1"   "RP11-124B13.1"
## [33] "RP11-511B23.2" "PRANCR"        "RP11-260G13.1" "LINC01572"    
## [37] "RP11-397A16.1" "AC005786.7"    "LINC00907"     "RP11-290O12.2"
## [41] "RP11-69G16.2"  "RP4-681L3.3"   "RP11-725F23.1" "RP11-314E10.1"

## [1] 5
##  [1] "MT1G"          "MTERF1"        "TMEM241"       "RERG"         
##  [5] "MT1E"          "DLEU1"         "LINC01006"     "HDHD5-AS1"    
##  [9] "CC2D2B"        "LEKR1"         "DIO2"          "HEPN1"        
## [13] "PLCG1-AS1"     "SOX21-AS1"     "HDAC2-AS2"     "LINC01344"    
## [17] "RP4-613B23.1"  "RP1-45C12.1"   "LINC01937"     "RP11-142A5.1" 
## [21] "AC079305.11"   "LINC02652"     "PKN2-AS1"      "H2AZ1-DT"     
## [25] "MEF2C-AS2"     "LINC02234"     "HS3ST5"        "LINC01340"    
## [29] "LINC01950"     "RP11-404I7.2"  "LIX1-AS1"      "RP1-84O15.2"  
## [33] "LINC00534"     "RP11-804N13.1" "RP11-431M3.1"  "RP11-526N18.1"
## [37] "RP11-242P2.1"  "LINC00637"     "RP11-103J8.1"  "LINC00540"    
## [41] "LINC01727"     "RP11-589M4.5"  "RP3-383B8.1"   "RP11-346I3.7" 
## [45] "RP11-399K19.1"

## [1] 6
##  [1] "ARHGAP44"       "SNCAIP"         "MROH8"          "PUDP"          
##  [5] "KCTD1"          "FADS2"          "EFCAB11"        "SLC14A1"       
##  [9] "TEX9"           "MAP3K7CL"       "STPG2"          "LMOD1"         
## [13] "RFLNA"          "ADAP2"          "SLC24A3"        "ADD3-AS1"      
## [17] "LIPE-AS1"       "COL28A1"        "LINC00571"      "LMCD1-AS1"     
## [21] "AC097721.2"     "RP11-498J9.2"   "LINC02884"      "RAP2C-AS1"     
## [25] "RP11-120D5.1"   "RPL34-DT"       "LINC00886"      "SUCLG2-AS1"    
## [29] "RP11-461O7.1"   "RP11-11N9.4"    "RP11-130F10.1"  "RP11-284M14.1" 
## [33] "RP11-582J16.4"  "RP11-20I20.2"   "RP11-727A23.10" "SPESP1"        
## [37] "RP11-739G5.1"   "PLS3-AS1"       "SYNPO2L-AS1"    "RP1-84D21.2"   
## [41] "RNF19A"         "NOL4L"          "ZNF358"

## [1] 7
##  [1] "DNAH9"    "BID"      "GAB2"     "FAM107B"  "SGK2"     "PLS3"    
##  [7] "SLC39A14" "SLC2A9"   "PPM1H"    "EEPD1"    "MASP1"    "PRR5L"   
## [13] "LPAR4"    "PTH1R"    "CA3"      "CERS6"    "NIPAL3"   "MAP3K9"  
## [19] "HDAC9"    "MAST3"    "SH3PXD2A" "IL1R1"    "ASL"      "ZFP36"   
## [25] "IRAK2"    "NAV1"     "KIAA0513" "EGF"      "MAGI1"    "DEPTOR"  
## [31] "MYO1E"    "TMEM200A" "IKBIP"    "SPSB1"    "MOB3A"    "PAWR"    
## [37] "OSTN"     "AFAP1"    "MEF2B"    "CPEB1"

## [1] 8
##  [1] "RP11-793A3.2"  "BAIAP3"        "TESC"          "DNAH11"       
##  [5] "USP9Y"         "LRAT"          "HELB"          "SCN1A"        
##  [9] "CCDC175"       "ANGPT1"        "SAMD3"         "ADCY1"        
## [13] "NLGN4Y"        "SLITRK5"       "NPNT"          "TTTY14"       
## [17] "CAVIN1"        "PLCXD3"        "CHST6"         "UTY"          
## [21] "SAMD11"        "OVCH1"         "LAMA2"         "S1PR3"        
## [25] "AP001347.6"    "TTTY10"        "RP11-469A15.2" "LINC00278"    
## [29] "RP1-187B23.1"  "RP11-146I2.1"  "IQCM"          "RP11-305L7.3" 
## [33] "CTD-2643I7.5"  "RP11-190P13.2" "RTL9"          "KCNK15-AS1"   
## [37] "RP11-259K15.2" "RP11-876N24.2" "RP11-60A24.3"  "MAFG-DT"      
## [41] "MIR23AHG"      "RP11-403A3.2"  "RP3-365E2.1"

## [1] 9
##  [1] "CD38"          "HHAT"          "ANKRD7"        "PAPPA2"       
##  [5] "TFAP2E"        "PLAGL1"        "RGS22"         "PEBP4"        
##  [9] "LIX1"          "CHODL"         "PKD1L1"        "KIF6"         
## [13] "FREM1"         "ALDH1A1"       "PRTG"          "VWA3B"        
## [17] "ODAD2"         "WDR97"         "ENO4"          "SCOC-AS1"     
## [21] "MAMDC2-AS1"    "CHL1-AS2"      "LINC01876"     "RP11-162D16.2"
## [25] "RP1-167A14.2"  "LINC01515"     "ZRANB2-AS2"    "RP11-195C7.1" 
## [29] "RP11-132E11.2" "LINC01358"     "CDKN2B-AS1"    "RP11-1252I4.2"
## [33] "RP4-785G19.5"  "LINC00958"     "CTC-347C20.1"  "CTB-178M22.2" 
## [37] "RP11-708B6.2"  "LINC02320"     "RP11-16B13.1"  "CRTC3-AS1"    
## [41] "RP11-525K10.3" "RP11-396B14.2" "LINC00506"     "RP11-175O15.1"

## [1] 10
##  [1] "USH1C"         "DPYSL3"        "UBE3D"         "COL4A2"       
##  [5] "MIPOL1"        "STOX2"         "GPC6"          "HMGN5"        
##  [9] "AC105760.2"    "RP11-550I24.2" "MALAT1"        "RP11-352M15.1"
## [13] "RARB"          "SLCO1A2"       "RFX2"          "P2RX7"        
## [17] "CDH20"         "MYOM1"         "FGL1"          "PPARGC1A"     
## [21] "LIN7A"         "RFX4"          "PRR12"         "IQCA1"        
## [25] "DMGDH"         "CCDC146"       "DPYSL5"        "TCAP"         
## [29] "FIGN"          "TSHZ2"         "FAM174B"       "TSBP1-AS1"    
## [33] "RP11-69I8.3"   "RP11-348F1.3"  "LINC00342"     "MIR4300HG"    
## [37] "RP11-279O9.4"  "TAPT1-AS1"     "SPANXA2-OT1"   "RP11-799O21.2"
## [41] "RP11-125C10.1"

## [1] 11
##  [1] "CLIC5"       "PDE8B"       "ACAT2"       "HS3ST3B1"    "HESX1"      
##  [6] "AF131217.1"  "AQP1"        "LRRC24"      "GTF2IRD1"    "ATP9A"      
## [11] "ITPKC"       "PIR"         "EBF4"        "CERS4"       "PLIN3"      
## [16] "ABCC3"       "ST8SIA1"     "ZC4H2"       "ZBTB46"      "GFAP"       
## [21] "TMCC2"       "CDR2"        "SSH2"        "FSIP1"       "RHPN1"      
## [26] "ARHGAP35"    "ZER1"        "SLC20A2"     "PTPN9"       "CLIC4"      
## [31] "IFFO2"       "NPAS2"       "PFKFB3"      "HAP1"        "SLC35E3"    
## [36] "SYNM"        "CMTM4"       "RILPL1"      "LIME1"       "FBXO17"     
## [41] "ATP6V0D1-DT"

## [1] 12
##  [1] "ANOS1"         "RRAGD"         "PSD"           "ATP11A"       
##  [5] "MAOB"          "ANKRD24"       "KIAA1549L"     "PHACTR2"      
##  [9] "TACR1"         "ELL2"          "MGAT3"         "UNC13A"       
## [13] "WARS1"         "SLC44A3"       "PRSS23"        "BEND6"        
## [17] "SPOCK1"        "ANKRD33B"      "METTL2B"       "HOPX"         
## [21] "PRELID2"       "PCLO"          "C9orf153"      "IER5L"        
## [25] "MAML3"         "FBXO16"        "CTA-292E10.6"  "OSMR-AS1"     
## [29] "TRMT9B"        "IDH2-DT"       "RP1-41C23.1"   "RP11-125D12.3"
## [33] "CTD-2126E3.6"  "KLF6"          "P3H2"          "COL5A1"       
## [37] "TMTC1"         "ZNF208"        "ARHGEF3"       "TPST1"        
## [41] "RGS6"          "TCEA3"         "RP11-513I15.6" "PCAT1"

## [1] 13
##  [1] "SPATA6L"       "SLC16A6"       "WNT5B"         "PDE10A"       
##  [5] "GDAP1L1"       "IFI44L"        "FHAD1"         "SLC22A3"      
##  [9] "DUSP15"        "ERICH3"        "CCBE1"         "LGALSL-DT"    
## [13] "TARID"         "LINC01768"     "RP1-223B1.1"   "LINC00326"    
## [17] "KIF5C-AS1"     "LINC01503"     "NPIPB2"        "LINC00877"    
## [21] "CXXC4-AS1"     "BAALC-AS1"     "C5orf17"       "RP11-380P13.1"
## [25] "LINC00923"     "RP11-745L13.2" "CENATAC-DT"    "MTRNR2L8"     
## [29] "MAP1LC3B2"     "HIF1A-AS3"     "RP11-798K3.2"  "DISC1FP1"     
## [33] "AC007193.6"    "LINC01374"     "RP11-496B10.6" "RP11-364P22.4"
## [37] "RP11-492O8.3"  "CTD-2040G12.2" "AC006296.4"    "RP11-520F22.1"
## [41] "RP11-215I16.3" "KRTAP5-AS1"

## [1] 14
##  [1] "MOGAT1"         "TMEM132B"       "SYCP2L"         "UNC5D"         
##  [5] "SGCD"           "MACROD2"        "OBI1-AS1"       "RP11-154H17.1" 
##  [9] "MGAM"           "RP11-111A21.1"  "RP11-571L19.7"  "CTD-2349P21.11"
## [13] "COL5A3"         "DAAM1"          "NCAN"           "ZSWIM6"        
## [17] "ADGRB3"         "GLTP"           "TENM2"          "JAZF1"         
## [21] "NRG2"           "ADORA1"         "NAV2"           "CHST11"        
## [25] "LRRC8C"         "CADM2"          "CALCB"          "LDLRAD3"       
## [29] "SLC25A18"       "MAML2"          "FLRT2"          "PLK5"          
## [33] "ZNF98"          "AP000318.2"     "DLEU2"          "PTCHD1-AS"     
## [37] "AC002127.4"     "MEIKIN"         "LINC01252"      "STX18-AS1"     
## [41] "TMEM161B-AS1"   "AGBL1"          "RP11-358F13.1"

## [1] 15
##  [1] "IQCH"        "TACC2"       "THSD4"       "VCAN"        "COL23A1"    
##  [6] "SYNE2"       "EEF2K"       "SUSD1"       "CCL2"        "WASF1"      
## [11] "ARSB"        "KLHL29"      "MOB3B"       "TSHZ3"       "HIVEP3"     
## [16] "QRICH2"      "GALNT8"      "PTPRE"       "PLCE1"       "COL6A2"     
## [21] "CLVS2"       "ITPRIP"      "CNKSR2"      "ARID5B"      "SEC24D"     
## [26] "RASSF3"      "ORAI2"       "ELAPOR2"     "TMC1"        "FBN1"       
## [31] "FRMD3"       "RCAN2"       "SPACA6"      "ZBTB7C"      "MITF"       
## [36] "NHS"         "COL27A1"     "RASGEF1A"    "NHSL2"       "LINC00685"  
## [41] "L3MBTL2-AS1" "LINC00609"

## [1] 16
##  [1] "CD200R1"        "FAP"            "LAMB4"          "KLF2"          
##  [5] "LGR6"           "AK7"            "LRMDA"          "KCNE4"         
##  [9] "GAL3ST2"        "TDRD9"          "ESYT3"          "PPP1R36"       
## [13] "METTL7B"        "SLC26A5"        "NOTUM"          "TRDN"          
## [17] "C3orf35"        "LINC00862"      "RP11-174G6.1"   "ARL17B"        
## [21] "RP5-1198O20.4"  "SPRY4-AS1"      "LINC01137"      "KCNMB2-AS1"    
## [25] "RP11-446J8.1"   "LINC02315"      "RP11-346L1.2"   "RP11-150C16.1" 
## [29] "RP11-328J6.1"   "RP11-499F3.2"   "CEACAM16-AS1"   "KLF2-DT"       
## [33] "MTRNR2L12"      "RP11-711K1.8"   "RP11-154H23.4"  "LINC02246"     
## [37] "RP11-114N1.1"   "RP1-166D18.1"   "RP11-465L10.14" "CTD-2201E18.6" 
## [41] "RP11-103P4.1"

## [1] 17
##  [1] "ID1"           "SLC7A2"        "SAMD4A"        "APBA2"        
##  [5] "SEMA3C"        "FOSL2"         "SESN1"         "PCSK5"        
##  [9] "GADD45B"       "RNF24"         "CAB39L"        "KAT8"         
## [13] "SPAG1"         "AGFG2"         "BACH2"         "TFDP2"        
## [17] "ID3"           "FOXO3"         "JUND"          "SLC39A11"     
## [21] "ARHGAP29"      "TIAM2"         "CREB5"         "SEMA3D"       
## [25] "SHISA5"        "NFIL3"         "CKB"           "ZNF608"       
## [29] "FOS"           "JUNB"          "ANO6"          "MAFF"         
## [33] "ZFP36L1"       "DMWD"          "IRS2"          "EFCAB2"       
## [37] "C19orf38"      "AC003991.3"    "RP11-507B12.1" "RP11-166M16.1"
## [41] "RP11-404C6.6"

## [1] 18
##  [1] "NRXN3"          "LRRC7"          "STS"            "IL7"           
##  [5] "EPM2A"          "LAMA4"          "PPP1R3C"        "BCL2L14"       
##  [9] "MT2A"           "CALY"           "UNC79"          "PDE5A"         
## [13] "ABCA12"         "SUMF1"          "GRIK2"          "HNF4G"         
## [17] "JAM3"           "PLD5"           "PNMA3"          "KIAA0825"      
## [21] "NAP1L3"         "EYS"            "CARNMT1-AS1"    "TENM3"         
## [25] "AC072062.3"     "SNHG31"         "MIR181A1HG"     "LINC00407"     
## [29] "SOX2-OT"        "LINC00504"      "SEMA6A-AS1"     "LINC02326"     
## [33] "RP11-57G22.3"   "RP11-1289C17.1" "RP11-335E8.3"   "GAS7"          
## [37] "RHOBTB1"        "PXDNL"          "PGM2L1"         "NLGN1"         
## [41] "DPYD"

## [1] 19
##  [1] "SPATA17"       "DNAH12"        "RP1-230L10.1"  "RP11-788A4.3" 
##  [5] "CP"            "ST6GALNAC2"    "PRRX1"         "SOHLH2"       
##  [9] "HNMT"          "LMNTD1"        "LRGUK"         "DRC1"         
## [13] "CFAP251"       "VWA5B1"        "ABCA1"         "CFAP47"       
## [17] "ARMC3"         "TVP23A"        "TEKT1"         "ATOH8"        
## [21] "GSG1L"         "COL24A1"       "PPP1R42"       "CCDC30"       
## [25] "CFAP54"        "TOGARAM2"      "TRPV1"         "WARS2-AS1"    
## [29] "LINC01135"     "RP11-90C4.1"   "LINC01411"     "LINC01088"    
## [33] "CTB-35F21.1"   "RP11-148E17.1" "RP11-627D16.1" "CTD-2054N24.2"
## [37] "RP11-210M15.2" "RP11-838N2.5"  "RP11-35G9.5"   "RP11-114N19.3"
## [41] "RP11-301F14.1" "RP11-6L16.1"

## [1] 20
##  [1] "DHRS7B"   "ABCC4"    "FAXC"     "IGFBP7"   "DPP10"    "ARHGAP31"
##  [7] "RRP12"    "PDE4A"    "PDK3"     "PHACTR3"  "MYO9B"    "COTL1"   
## [13] "SYT17"    "SGK1"     "HIF3A"    "HIP1"     "RIN2"     "ARHGEF4" 
## [19] "BCAS3"    "NFIC"     "ENSA"     "KCNN3"    "ITPKB"    "ARHGAP26"
## [25] "DOCK11"   "GRIK4"    "NCAM2"    "C2CD2"    "ABR"      "DHRS3"   
## [31] "ZNF704"   "WNK2"     "GNG4"     "KCND3"    "FAM222B"  "SYT12"   
## [37] "SH3PXD2B" "PHYHD1"   "CTXN1"    "APOLD1"   "ANKS1B"   "SRGAP1"

## [1] 21
##  [1] "FAR2"       "SEZ6L"      "ZFR2"       "GABRA4"     "RGS4"      
##  [6] "RFC3"       "BEX1"       "TESPA1"     "RNF165"     "GULP1"     
## [11] "ARHGAP18"   "CCDC102B"   "BTBD11"     "PLEKHG4B"   "SYNPR"     
## [16] "NDST3"      "TMEM130"    "ZNF497"     "KCNB2"      "STAC3"     
## [21] "SLIT1"      "COL25A1"    "IL1RAPL2"   "PIWIL2"     "AC011288.2"
## [26] "BAALC-AS2"  "PWRN1"      "KCNG1"      "CDH3"       "ZFY"       
## [31] "TRHDE"      "ARHGAP15"   "KHDRBS2"    "KIAA1217"   "HS3ST2"    
## [36] "DOCK10"     "SRRM4"      "KCNH5"      "RIT2"       "ZMAT4"     
## [41] "NABP1"      "VSTM2B"

## [1] 22
##  [1] "PRKCQ"         "F3"            "DPH6"          "ST6GAL2"      
##  [5] "SLC9B1"        "OTOGL"         "CYP7B1"        "CASC2"        
##  [9] "CATSPERE"      "GPR39"         "DCHS2"         "MALRD1"       
## [13] "AC004540.5"    "LINC02649"     "SOX1-OT"       "POT1-AS1"     
## [17] "LYPLAL1-DT"    "XIST"          "AC079807.4"    "LINC00271"    
## [21] "AC007682.1"    "RFX3-AS1"      "UFL1-AS1"      "COX10-AS1"    
## [25] "RNF217-AS1"    "RP11-4B14.3"   "LINC02144"     "RP11-268P4.5" 
## [29] "LINC01182"     "RP11-679C8.2"  "GS1-57L11.1"   "RP11-541P9.3" 
## [33] "RMST"          "RP11-20E24.1"  "RP11-72M17.1"  "LINC02328"    
## [37] "PSMD7-DT"      "CTC-498M16.4"  "RP11-444C24.1" "RP11-221G19.1"
## [41] "RP11-96C13.1"  "RP4-660H19.2"  "RP11-563M4.2"

## [1] 23
##  [1] "MBNL3"      "GFRA1"      "PDZD4"      "RBFOX1"     "CELF4"     
##  [6] "TUSC3"      "PPP1R13L"   "CHRNE"      "TSPAN11"    "PDE1A"     
## [11] "B4GALT2"    "NRP2"       "ACVR1C"     "LRRC4B"     "DGKB"      
## [16] "TTLL7"      "SLC44A5"    "RHBDL3"     "ZNF385B"    "DIAPH2"    
## [21] "SNTG1"      "CACNA1B"    "CLSTN2"     "EDIL3"      "OXR1"      
## [26] "FAT3"       "FAAH2"      "RBFOX3"     "PDE3A"      "ARPP21"    
## [31] "DAB1"       "ST8SIA3"    "SLC25A20"   "GPR137C"    "ZNF804B"   
## [36] "DUSP8"      "KBTBD12"    "PAX8-AS1"   "PTPRT"      "LYRM4"     
## [41] "CYP1B1-AS1" "ETV5"       "LINC01414"

## [1] 24
##  [1] "RNF175"           "KIRREL3"          "MMP16"            "GRIK1"           
##  [5] "GALNTL6"          "GRM7"             "RP11-170M17.1"    "MSC-AS1"         
##  [9] "RP4-809F18.1"     "RP11-640F22.1"    "RP11-320L2.1"     "SYT7"            
## [13] "SEC14L5"          "ATRNL1"           "RIMS3"            "SCN2A"           
## [17] "CBLN2"            "SLC4A10"          "CDH18"            "CNTN5"           
## [21] "PLCL2"            "SLC24A2"          "CFAP161"          "LRRC2"           
## [25] "HTR1E"            "SLC38A11"         "RIMS2"            "SLC8A1"          
## [29] "KCNH7"            "PDE2A"            "CACNA1E"          "LINC00632"       
## [33] "TNFRSF25"         "RP11-191L9.4"     "XXbac-BPG55C20.7" "RP1-30E17.2"     
## [37] "SHISA9"           "CTC-340A15.2"     "LINC01322"        "PTCHD4"          
## [41] "LINC02223"        "RP11-624C23.1"    "IQCJ-SCHIP1"

## [1] 25
##  [1] "EPHA6"       "TRPM3"       "SCG3"        "EYA1"        "SLC1A2"     
##  [6] "EYA4"        "DNAH7"       "CABLES1"     "CXCL14"      "ACSL1"      
## [11] "AXDND1"      "KLHL32"      "GRM3"        "CNTN1"       "ATP1A2"     
## [16] "MCF2L2"      "DGKG"        "KIF3C"       "CPEB3"       "CCND3"      
## [21] "C1orf21"     "PDZRN3"      "TOX2"        "SYNE1"       "CEP350"     
## [26] "SHROOM3"     "FAM171A1"    "FAM13C"      "PID1"        "GNA14"      
## [31] "AHCYL2"      "CACNB2"      "CACNB3"      "ZFPM2"       "NCKAP5"     
## [36] "CNTN2"       "EFNA5"       "TPCN1"       "ZNF785"      "TOX"        
## [41] "ALDH1L1-AS2"

## [1] 26
##  [1] "MRC2"          "TNC"           "MSMO1"         "IDI1"         
##  [5] "REEP1"         "SRPX"          "RIPK2"         "RASD1"        
##  [9] "NT5DC3"        "B3GAT2"        "HMGCS1"        "CRISPLD1"     
## [13] "ADCY7"         "TRIM5"         "PLXNC1"        "ARRDC4"       
## [17] "CHST9"         "ABI3BP"        "FABP5"         "SVEP1"        
## [21] "SCG5"          "GINS3"         "PAPPA"         "PROS1"        
## [25] "INSIG1"        "F5"            "RP11-106M7.1"  "DPP10-AS3"    
## [29] "LINC01524"     "AC007563.5"    "RP11-239A17.1" "RP11-274G22.1"
## [33] "RP11-373E16.6" "KITLG"         "FRY"           "CLSTN3"       
## [37] "PARP8"         "SHTN1"         "SMOC1"         "CRYBB2"       
## [41] "RP11-542F9.2"

## [1] 27
##  [1] "AMPH"     "BLVRB"    "APBA1"    "SH3D19"   "GMDS"     "GBE1"    
##  [7] "HSPH1"    "ALCAM"    "EXT1"     "CMSS1"    "BRINP2"   "MRPL33"  
## [13] "ITGA3"    "SYN1"     "EYA2"     "RASAL2"   "DOK5"     "ARHGEF18"
## [19] "OLFM2"    "DNM1"     "VAV3"     "CCNH"     "BIN1"     "SLC22A23"
## [25] "MINK1"    "GABPB2"   "SDK1"     "DGKZ"     "PTPRJ"    "ADAM33"  
## [31] "DOC2A"    "THRB"     "SPTBN4"   "PKNOX2"   "PLEKHA7"  "PCDH7"   
## [37] "REPS2"    "RPS6KA3"  "PARVA"    "PLCG2"    "DNM3"

## [1] 28
##  [1] "LINC02217"               "SLC26A3"                
##  [3] "CACNA1I"                 "KLHL4"                  
##  [5] "STEAP1B"                 "BEST3"                  
##  [7] "UNC13C"                  "ST18"                   
##  [9] "SHROOM4"                 "SYTL3"                  
## [11] "GREM1"                   "SEMA3E"                 
## [13] "RTN4RL1"                 "AC023469.1"             
## [15] "AC003090.1"              "RP11-563D10.1"          
## [17] "RP1-35C21.2"             "LINC01320"              
## [19] "SATB1-AS1"               "RP11-147G16.1"          
## [21] "RP11-154D17.1"           "AC013463.2"             
## [23] "RP5-827C21.2"            "AC002066.1"             
## [25] "RP11-384F7.1"            "RP11-17A1.3"            
## [27] "LINC02742"               "RP11-79E3.2"            
## [29] "LINC01609"               "RP11-958J22.1"          
## [31] "RP11-20D14.3"            "RPPH1_ENSG00000259001"  
## [33] "LINC00558"               "AF038458.3"             
## [35] "RMRP_ENSG00000269900"    "SCARNA2_ENSG00000270066"
## [37] "CH507-513H4.1"           "CH507-528H12.1"         
## [39] "RP11-596C23.6"           "RP4-799O8.1"            
## [41] "AC003099.2"              "RP5-1015P16.1"          
## [43] "RP11-398J12.1"           "RP11-4D11.1"

## [1] 29
##  [1] "CDON"           "ADGRL1"         "TMEM38A"        "GRK3"          
##  [5] "RIPOR2"         "PADI2"          "TICAM1"         "RAP1GAP2"      
##  [9] "NKD1"           "BOC"            "CCDC3"          "MRAS"          
## [13] "FBXO27"         "PTCHD1"         "FAXDC2"         "FZD8"          
## [17] "CTD-2527I21.15" "NME9"           "OSBP2"          "C7orf61"       
## [21] "NWD1"           "TMEM184B"       "PLIN5"          "LINC00598"     
## [25] "NRSN2-AS1"      "HPN-AS1"        "RP5-864K19.4"   "AC104088.1"    
## [29] "PDYN-AS1"       "AC016745.3"     "OLMALINC"       "DPH6-DT"       
## [33] "LINC02208"      "RP11-298I3.1"   "LINC02356"      "RP3-414A15.10" 
## [37] "RP11-507B12.2"  "CASC17"         "RP1-158P9.2"    "AC079610.1"    
## [41] "RP11-379B18.8"  "RP11-26L21.1"   "RP11-237N2.1"

## [1] 30
##  [1] "YBX3"    "NTN1"    "SRBD1"   "MT3"     "CEMIP"   "RPL18A"  "RPL19"  
##  [8] "RPS15"   "NID1"    "APOE"    "RPL36"   "TMEM160" "CCDC59"  "EMP1"   
## [15] "RPLP1"   "FAU"     "DLC1"    "ANO5"    "GLRX"    "A2M"     "RPS27"  
## [22] "LRRC3B"  "ZNF48"   "KCNMB2"  "RPS18"   "LUCAT1"  "VRK2"    "ICAM1"  
## [29] "WFDC1"   "XYLT1"   "KNOP1"   "KCNN1"   "LOXL1"   "EDA2R"   "FANCC"  
## [36] "FGF17"   "SLC5A11" "EVA1C"   "LINGO1"  "SWI5"    "S100A10"

## [1] 31
##  [1] "PNPLA3"                  "SLC24A4"                
##  [3] "DNAAF1"                  "PCED1B"                 
##  [5] "SLC4A5"                  "PATL2"                  
##  [7] "LINC02615"               "MAPT-AS1"               
##  [9] "RP5-965G21.3"            "RP11-574F11.4"          
## [11] "RP11-255O19.2"           "DNAH5"                  
## [13] "ST6GAL1"                 "CATSPERG"               
## [15] "RASL12"                  "AEBP1"                  
## [17] "CLIP2"                   "JHY"                    
## [19] "MAN1C1"                  "GFPT2"                  
## [21] "PATJ"                    "TTC9"                   
## [23] "GMPR"                    "DENND2A"                
## [25] "ADCY8"                   "ST3GAL2"                
## [27] "TMCO4"                   "C1orf87"                
## [29] "DEPP1"                   "PRIMA1"                 
## [31] "SLCO3A1"                 "SPATA13_ENSG00000182957"
## [33] "SLC6A9"                  "ODAD4"                  
## [35] "CFI"                     "RP1-111D6.3"            
## [37] "AC004951.6"              "EPCAM-DT"               
## [39] "HMGA1P4"                 "LINC01094"              
## [41] "ZNF594-DT"               "RP1-79C4.4"             
## [43] "CASTOR2"                 "RP11-514P8.10"

## [1] 32
##  [1] "UPP2"          "MAMLD1"        "PEX5L"         "ST6GALNAC5"   
##  [5] "BICC1"         "KIAA1328"      "C4orf19"       "C2CD6"        
##  [9] "FTH1"          "RNF150"        "ADRA1B"        "MTSS1"        
## [13] "NEGR1"         "SUGCT"         "TMEM132C"      "TAFA1"        
## [17] "WNT7B"         "FIRRE"         "APTR"          "LCNL1"        
## [21] "CRPPA"         "LINC01266"     "AP001628.6"    "PPP1R26-AS1"  
## [25] "AP000282.2"    "AC008269.2"    "MMADHC-DT"     "RP11-154D6.1" 
## [29] "PPP1R9A-AS1"   "RP11-390F4.6"  "DRAIC"         "RP11-373N22.3"
## [33] "CTB-161M19.4"  "LINC01301"     "RP11-673E1.1"  "RP11-317N12.1"
## [37] "RP11-134O21.1" "CTXND1"        "ADGRL1-AS1"    "GEMIN7-AS1"   
## [41] "RP11-157E16.1" "CTC-490G23.6"  "CPM"

## [1] 33
##  [1] "SP140"          "LINC01931"      "P2RY14"         "ZBTB44-DT"     
##  [5] "C12orf42"       "FSIP2"          "TSBP1"          "ANKUB1"        
##  [9] "AC002463.3"     "RP4-660H19.1"   "PCDH9-AS2"      "GPC5-AS2"      
## [13] "PCDH9-AS4"      "STARD13-AS"     "RP11-475C16.2"  "RP13-143G15.4" 
## [17] "LINC00960"      "RP11-768G7.3"   "LRP4-AS1"       "ANK2-AS1"      
## [21] "CTD-2015H6.3"   "RP11-669M16.1"  "MAPK10-AS1"     "RP11-517I3.1"  
## [25] "ZFPM2-AS1"      "RP11-116O11.1"  "RP11-351A11.1"  "BBOX1-AS1"     
## [29] "AP000462.2"     "RP11-513G19.1"  "RP11-370I10.2"  "RP11-39M21.1"  
## [33] "PRKCA-AS1"      "RP11-138H11.1"  "RP11-355F16.1"  "RP11-561I11.4" 
## [37] "CTD-2282P23.2"  "RP11-413N10.3"  "RP11-576O3.1"   "RP11-793H13.14"
## [41] "RP11-66G15.1"   "RP11-120J1.2"   "RP5-892C22.1"   "RP11-168F16.1"

## [1] 34
##  [1] "TENM1"   "GTDC1"   "TMEM108" "NDUFAF2" "GALNT10" "HPRT1"   "GPR156" 
##  [8] "IMMP2L"  "SMYD3"   "PTPRN"   "CAMK2B"  "RIMBP2"  "CTNNA2"  "PLXNA2" 
## [15] "TGFB2"   "GLIS3"   "UBE2R2"  "ZMIZ1"   "CLNK"    "TPD52L1" "STAG1"  
## [22] "MACF1"   "PALLD"   "SOX5"    "MAPK4"   "ECE2"    "PAM"     "ZEB1"   
## [29] "CNNM2"   "FOXO1"   "DST"     "ART3"    "STX8"    "BCL2"    "FRMD5"  
## [36] "CADM1"   "EML6"    "NEAT1"   "CUX1"

## [1] 35
##  [1] "XK"            "CALCRL"        "ARHGAP28"      "CCDC80"       
##  [5] "SLC8A3"        "PLCB4"         "TRIM22"        "FHDC1"        
##  [9] "LRRIQ3"        "ADAMTS9"       "GUCY1A1"       "GFRA2"        
## [13] "STK32A"        "DELEC1"        "SNX31"         "CIITA"        
## [17] "CYP4F12"       "CYP4F3"        "STUM"          "INSYN2B"      
## [21] "DIRC3"         "DIRC3-AS1"     "LINC02814"     "AC092684.1"   
## [25] "SOCS2-AS1"     "NEUROG2-AS1"   "RP11-364L4.3"  "RP11-116N8.1" 
## [29] "FRMD6-AS2"     "RP11-354K4.2"  "APP-DT"        "RP11-323P17.2"
## [33] "LINC00836"     "LINC00842"     "RP11-259G3.1"  "RP11-154D6.3" 
## [37] "RP11-609L3.3"  "RP1-20N4.2"    "RP11-423B13.1" "ARHGAP6"      
## [41] "NFASC"         "PLPP4"         "LINC02506"     "LINC02251"

## [1] 36
##  [1] "PON3"          "MAEL"          "MN1"           "PAH"          
##  [5] "RHCE"          "AC074391.1"    "EPS15-AS1"     "LNC-LBCS"     
##  [9] "LINC01185"     "LINC01277"     "LINC01239"     "NECTIN3-AS1"  
## [13] "LINC02196"     "F11-AS1"       "LINC00499"     "MAILR"        
## [17] "RP11-156K13.1" "RP11-266O8.1"  "AC004158.3"    "RP11-436D23.1"
## [21] "RP11-378A12.1" "CH17-174L20.1" "RP11-281A20.2" "RP11-437L7.2" 
## [25] "RP11-382N13.7" "RP11-692P14.1" "RP11-624A4.2"  "CTD-2297M2.1" 
## [29] "LGI1"          "TGIF2"         "KCNJ16"        "RFTN2"        
## [33] "RANBP3L"       "GPR176"        "C2"            "HPSE2"        
## [37] "IQCK"          "LHFPL6"        "AC064875.2"    "LINC00511"    
## [41] "ARHGEF26-AS1"  "CTD-2189E23.1" "RP11-183J19.1"

## [1] 37
##  [1] "SDK2"        "SYTL4"       "CAP2"        "WIPF1"       "ENOX1"      
##  [6] "FAM117B"     "C10orf90"    "ABHD3"       "NXN"         "SLC43A2"    
## [11] "LRRN2"       "TMEM51"      "SNTB1"       "C1QTNF4"     "CA8"        
## [16] "RNLS"        "ROR1"        "L3MBTL3"     "SAMD13"      "CTC-329D1.2"
## [21] "ATP2B4"      "TBC1D1"      "HSD17B14"    "PALM"        "COBL"       
## [26] "ZBTB16"      "WLS"         "SEM1"        "FCHO1"       "RFTN1"      
## [31] "TNS3"        "ADAMTS10"    "CTDSPL"      "ENOX2"       "FAM107A"    
## [36] "LDLRAD4"     "PACS1"       "GNG7"        "ABAT"        "HRH1"       
## [41] "KIF9-AS1"

## [1] 38
##  [1] "PRKAR2B"               "ELAVL2"                "MLIP"                 
##  [4] "LYPD6B"                "SHANK2"                "CADPS"                
##  [7] "RGS7"                  "KCTD16"                "CCSER1"               
## [10] "DLGAP2"                "RP11-410D17.2"         "SYT1"                 
## [13] "MAP2"                  "CPE"                   "CHD5"                 
## [16] "PLXDC2"                "DPP6"                  "ABCB9"                
## [19] "FAM151B"               "SHANK1"                "ZNF653"               
## [22] "ABLIM2"                "GRM5"                  "FRMPD4"               
## [25] "DLGAP1"                "CSDC2"                 "CNTNAP2"              
## [28] "PPM1E"                 "SAMD12"                "CSMD1"                
## [31] "GRIN2A"                "OPCML"                 "RALYL"                
## [34] "SYN3"                  "KCNQ5"                 "KCNIP4"               
## [37] "NKAIN2"                "ELAVL3"                "AJAP1"                
## [40] "RYR2"                  "MEG3"                  "DGCR5_ENSG00000273032"

## [1] 39
##  [1] "HSD11B1"      "IFI6"         "GPNMB"        "PLK2"         "ZCCHC18"     
##  [6] "RAB39A"       "SP140L"       "PDXP"         "LINC02254"    "USH2A"       
## [11] "NGEF"         "RASGRP2"      "ANGPT2"       "PCDH11Y"      "IGSF21"      
## [16] "TNNT2"        "TBX2"         "ITIH5"        "AIF1L"        "C1QL1"       
## [21] "SLC6A6"       "TBX6"         "CATIP"        "SPATA2L"      "PTMS"        
## [26] "COX7A1"       "VAT1L"        "NXNL1"        "MRGPRF"       "YOD1"        
## [31] "PCP4"         "FAM110C"      "POTEG"        "FZD9"         "STARD10"     
## [36] "LINC01208"    "HRAT92"       "LINC02869"    "AC067956.1"   "MTRNR2L1"    
## [41] "LINC01619"    "PKD1L3"       "RP11-93B21.2"

## [1] 40
##  [1] "BCAS1"         "PCSK1N"        "LRRC9"         "LRTM1"        
##  [5] "HHIP"          "CLMP"          "NRG4"          "SEPTIN1"      
##  [9] "CYP4X1"        "AC026188.1"    "LINC01117"     "AC105461.1"   
## [13] "Z83001.1"      "CCDC26"        "RP11-141A19.1" "IPO9-AS1"     
## [17] "LINC01725"     "LINC01877"     "RP11-446H18.5" "RP11-114J13.1"
## [21] "VCAN-AS1"      "RP11-348J24.1" "RP11-711G10.1" "STPG2-AS1"    
## [25] "RP11-586K2.1"  "RP11-649G15.2" "AB015752.3"    "RP11-624D11.2"
## [29] "LINC02389"     "RP11-867G2.8"  "RP11-315E17.1" "RP11-104E19.1"
## [33] "LINC01579"     "PTCSC3"        "RP11-184D12.1" "TSIX"         
## [37] "LINC02664"     "RP11-80I3.1"   "SLC7A14-AS1"   "CTC-428H11.2" 
## [41] "RP5-847G17.1"  "CTD-2172F7.1"  "RP11-875G18.1" "CCK"          
## [45] "AC092155.4"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_17"
##  [1] "ID1"           "SLC7A2"        "SAMD4A"        "APBA2"        
##  [5] "SEMA3C"        "FOSL2"         "SESN1"         "PCSK5"        
##  [9] "GADD45B"       "RNF24"         "CAB39L"        "KAT8"         
## [13] "SPAG1"         "AGFG2"         "BACH2"         "TFDP2"        
## [17] "ID3"           "FOXO3"         "JUND"          "SLC39A11"     
## [21] "ARHGAP29"      "TIAM2"         "CREB5"         "SEMA3D"       
## [25] "SHISA5"        "NFIL3"         "CKB"           "ZNF608"       
## [29] "FOS"           "JUNB"          "ANO6"          "MAFF"         
## [33] "ZFP36L1"       "DMWD"          "IRS2"          "EFCAB2"       
## [37] "C19orf38"      "AC003991.3"    "RP11-507B12.1" "RP11-166M16.1"
## [41] "RP11-404C6.6" 
## $reactome
##                                                      category
## 604                              ngf stimulated transcription
## 947                                        signaling by ntrks
## 626 nuclear events kinase and transcription factor activation
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 604            1.470466e-06                1.0000000          5       10
## 947            5.745032e-06                0.9999997          7       25
## 626            1.519618e-05                0.9999995          5       13
##             FDR
## 604 0.001651333
## 947 0.003225835
## 626 0.005688436
## 
## [1] "set_19"
##  [1] "SPATA17"       "DNAH12"        "RP1-230L10.1"  "RP11-788A4.3" 
##  [5] "CP"            "ST6GALNAC2"    "PRRX1"         "SOHLH2"       
##  [9] "HNMT"          "LMNTD1"        "LRGUK"         "DRC1"         
## [13] "CFAP251"       "VWA5B1"        "ABCA1"         "CFAP47"       
## [17] "ARMC3"         "TVP23A"        "TEKT1"         "ATOH8"        
## [21] "GSG1L"         "COL24A1"       "PPP1R42"       "CCDC30"       
## [25] "CFAP54"        "TOGARAM2"      "TRPV1"         "WARS2-AS1"    
## [29] "LINC01135"     "RP11-90C4.1"   "LINC01411"     "LINC01088"    
## [33] "CTB-35F21.1"   "RP11-148E17.1" "RP11-627D16.1" "CTD-2054N24.2"
## [37] "RP11-210M15.2" "RP11-838N2.5"  "RP11-35G9.5"   "RP11-114N19.3"
## [41] "RP11-301F14.1" "RP11-6L16.1"  
## $go_bp
##                                        category over_represented_pvalue
## 560 cilium or flagellum dependent cell motility            9.377027e-06
##     under_represented_pvalue numDEInCat numInCat        FDR
## 560                0.9999997          5       19 0.04210285
## 
## [1] "set_20"
##  [1] "DHRS7B"   "ABCC4"    "FAXC"     "IGFBP7"   "DPP10"    "ARHGAP31"
##  [7] "RRP12"    "PDE4A"    "PDK3"     "PHACTR3"  "MYO9B"    "COTL1"   
## [13] "SYT17"    "SGK1"     "HIF3A"    "HIP1"     "RIN2"     "ARHGEF4" 
## [19] "BCAS3"    "NFIC"     "ENSA"     "KCNN3"    "ITPKB"    "ARHGAP26"
## [25] "DOCK11"   "GRIK4"    "NCAM2"    "C2CD2"    "ABR"      "DHRS3"   
## [31] "ZNF704"   "WNK2"     "GNG4"     "KCND3"    "FAM222B"  "SYT12"   
## [37] "SH3PXD2B" "PHYHD1"   "CTXN1"    "APOLD1"   "ANKS1B"   "SRGAP1"  
## $reactome
##               category over_represented_pvalue under_represented_pvalue
## 116 cdc42 gtpase cycle            3.585973e-05                0.9999973
## 739  rac1 gtpase cycle            4.742297e-05                0.9999962
##     numDEInCat numInCat      FDR
## 116          7       23 0.026628
## 739          7       26 0.026628
## 
## [1] "set_24"
##  [1] "RNF175"           "KIRREL3"          "MMP16"            "GRIK1"           
##  [5] "GALNTL6"          "GRM7"             "RP11-170M17.1"    "MSC-AS1"         
##  [9] "RP4-809F18.1"     "RP11-640F22.1"    "RP11-320L2.1"     "SYT7"            
## [13] "SEC14L5"          "ATRNL1"           "RIMS3"            "SCN2A"           
## [17] "CBLN2"            "SLC4A10"          "CDH18"            "CNTN5"           
## [21] "PLCL2"            "SLC24A2"          "CFAP161"          "LRRC2"           
## [25] "HTR1E"            "SLC38A11"         "RIMS2"            "SLC8A1"          
## [29] "KCNH7"            "PDE2A"            "CACNA1E"          "LINC00632"       
## [33] "TNFRSF25"         "RP11-191L9.4"     "XXbac-BPG55C20.7" "RP1-30E17.2"     
## [37] "SHISA9"           "CTC-340A15.2"     "LINC01322"        "PTCHD4"          
## [41] "LINC02223"        "RP11-624C23.1"    "IQCJ-SCHIP1"     
## $go_bp
##                                    category over_represented_pvalue
## 3799 regulation of trans synaptic signaling            9.196575e-06
##      under_represented_pvalue numDEInCat numInCat        FDR
## 3799                 0.999999         10       97 0.04129262
## 
## [1] "set_26"
##  [1] "MRC2"          "TNC"           "MSMO1"         "IDI1"         
##  [5] "REEP1"         "SRPX"          "RIPK2"         "RASD1"        
##  [9] "NT5DC3"        "B3GAT2"        "HMGCS1"        "CRISPLD1"     
## [13] "ADCY7"         "TRIM5"         "PLXNC1"        "ARRDC4"       
## [17] "CHST9"         "ABI3BP"        "FABP5"         "SVEP1"        
## [21] "SCG5"          "GINS3"         "PAPPA"         "PROS1"        
## [25] "INSIG1"        "F5"            "RP11-106M7.1"  "DPP10-AS3"    
## [29] "LINC01524"     "AC007563.5"    "RP11-239A17.1" "RP11-274G22.1"
## [33] "RP11-373E16.6" "KITLG"         "FRY"           "CLSTN3"       
## [37] "PARP8"         "SHTN1"         "SMOC1"         "CRYBB2"       
## [41] "RP11-542F9.2" 
## $go_bp
##                         category over_represented_pvalue
## 4220 sterol biosynthetic process            5.056125e-06
##      under_represented_pvalue numDEInCat numInCat      FDR
## 4220                        1          4        6 0.022702
## 
## [1] "set_30"
##  [1] "YBX3"    "NTN1"    "SRBD1"   "MT3"     "CEMIP"   "RPL18A"  "RPL19"  
##  [8] "RPS15"   "NID1"    "APOE"    "RPL36"   "TMEM160" "CCDC59"  "EMP1"   
## [15] "RPLP1"   "FAU"     "DLC1"    "ANO5"    "GLRX"    "A2M"     "RPS27"  
## [22] "LRRC3B"  "ZNF48"   "KCNMB2"  "RPS18"   "LUCAT1"  "VRK2"    "ICAM1"  
## [29] "WFDC1"   "XYLT1"   "KNOP1"   "KCNN1"   "LOXL1"   "EDA2R"   "FANCC"  
## [36] "FGF17"   "SLC5A11" "EVA1C"   "LINGO1"  "SWI5"    "S100A10"
## $reactome
##                                                         category
## 287                            eukaryotic translation elongation
## 288                            eukaryotic translation initiation
## 610                                  nonsense mediated decay nmd
## 810            response of eif2ak4 gcn2 to amino acid deficiency
## 878                                  selenoamino acid metabolism
## 856                                              rrna processing
## 975  srp dependent cotranslational protein targeting to membrane
## 429                                          influenza infection
## 1078                                                 translation
## 762                  regulation of expression of slits and robos
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 287             1.136754e-11                        1          8        9
## 288             1.136754e-11                        1          8        9
## 610             1.136754e-11                        1          8        9
## 810             6.292460e-11                        1          8       10
## 878             7.081812e-11                        1          8       10
## 856             7.229398e-11                        1          8       10
## 975             2.493638e-10                        1          8       11
## 429             2.510579e-10                        1          8       11
## 1078            1.935771e-09                        1          8       13
## 762             2.057827e-09                        1          8       13
##               FDR
## 287  4.255248e-09
## 288  4.255248e-09
## 610  4.255248e-09
## 810  1.353102e-08
## 878  1.353102e-08
## 856  1.353102e-08
## 975  3.524226e-08
## 429  3.524226e-08
## 1078 2.310939e-07
## 762  2.310939e-07
## 
## $go_bp
##                    category over_represented_pvalue under_represented_pvalue
## 618 cytoplasmic translation                       0                        1
##     numDEInCat numInCat FDR
## 618          9       12   0
## 
## [1] "set_38"
##  [1] "PRKAR2B"               "ELAVL2"                "MLIP"                 
##  [4] "LYPD6B"                "SHANK2"                "CADPS"                
##  [7] "RGS7"                  "KCTD16"                "CCSER1"               
## [10] "DLGAP2"                "RP11-410D17.2"         "SYT1"                 
## [13] "MAP2"                  "CPE"                   "CHD5"                 
## [16] "PLXDC2"                "DPP6"                  "ABCB9"                
## [19] "FAM151B"               "SHANK1"                "ZNF653"               
## [22] "ABLIM2"                "GRM5"                  "FRMPD4"               
## [25] "DLGAP1"                "CSDC2"                 "CNTNAP2"              
## [28] "PPM1E"                 "SAMD12"                "CSMD1"                
## [31] "GRIN2A"                "OPCML"                 "RALYL"                
## [34] "SYN3"                  "KCNQ5"                 "KCNIP4"               
## [37] "NKAIN2"                "ELAVL3"                "AJAP1"                
## [40] "RYR2"                  "MEG3"                  "DGCR5_ENSG00000273032"
## $reactome
##                                     category over_represented_pvalue
## 595                neurexins and neuroligins            1.081398e-07
## 596                          neuronal system            1.284096e-07
## 725 protein protein interactions at synapses            1.098913e-06
##     under_represented_pvalue numDEInCat numInCat          FDR
## 595                        1          7       18 7.210198e-05
## 596                        1         11       72 7.210198e-05
## 725                        1          7       25 4.113598e-04
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8955042 478.3   16112782 860.6         NA 15574709 831.8
## Vcells 16666262 127.2   31262822 238.6      65536 31262822 238.6
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] goseq_1.50.0           geneLenDataBase_1.34.0 BiasedUrn_2.0.10      
##  [4] fgsea_1.24.0           biomaRt_2.54.1         limma_3.54.2          
##  [7] tidyr_1.3.0            ggpubr_0.6.0           ggplot2_3.4.2         
## [10] data.table_1.14.8     
## 
## loaded via a namespace (and not attached):
##   [1] nlme_3.1-162                matrixStats_1.0.0          
##   [3] bitops_1.0-7                bit64_4.0.5                
##   [5] filelock_1.0.2              progress_1.2.2             
##   [7] httr_1.4.6                  GenomeInfoDb_1.34.9        
##   [9] tools_4.2.3                 backports_1.4.1            
##  [11] bslib_0.4.2                 utf8_1.2.3                 
##  [13] R6_2.5.1                    mgcv_1.8-42                
##  [15] DBI_1.1.3                   BiocGenerics_0.44.0        
##  [17] colorspace_2.1-0            withr_2.5.0                
##  [19] tidyselect_1.2.0            prettyunits_1.1.1          
##  [21] bit_4.0.5                   curl_5.0.1                 
##  [23] compiler_4.2.3              cli_3.6.1                  
##  [25] Biobase_2.58.0              xml2_1.3.4                 
##  [27] DelayedArray_0.24.0         rtracklayer_1.58.0         
##  [29] sass_0.4.5                  scales_1.2.1               
##  [31] rappdirs_0.3.3              Rsamtools_2.14.0           
##  [33] stringr_1.5.0               digest_0.6.31              
##  [35] rmarkdown_2.21              XVector_0.38.0             
##  [37] pkgconfig_2.0.3             htmltools_0.5.5            
##  [39] MatrixGenerics_1.10.0       dbplyr_2.3.2               
##  [41] fastmap_1.1.1               rlang_1.1.0                
##  [43] rstudioapi_0.14             RSQLite_2.3.1              
##  [45] BiocIO_1.8.0                jquerylib_0.1.4            
##  [47] generics_0.1.3              jsonlite_1.8.4             
##  [49] BiocParallel_1.32.6         dplyr_1.1.2                
##  [51] car_3.1-2                   RCurl_1.98-1.12            
##  [53] magrittr_2.0.3              GO.db_3.16.0               
##  [55] GenomeInfoDbData_1.2.9      Matrix_1.6-4               
##  [57] Rcpp_1.0.10                 munsell_0.5.0              
##  [59] S4Vectors_0.36.2            fansi_1.0.4                
##  [61] abind_1.4-5                 lifecycle_1.0.3            
##  [63] stringi_1.7.12              yaml_2.3.7                 
##  [65] carData_3.0-5               SummarizedExperiment_1.28.0
##  [67] zlibbioc_1.44.0             org.Hs.eg.db_3.16.0        
##  [69] BiocFileCache_2.6.1         grid_4.2.3                 
##  [71] blob_1.2.4                  parallel_4.2.3             
##  [73] crayon_1.5.2                lattice_0.20-45            
##  [75] splines_4.2.3               Biostrings_2.66.0          
##  [77] cowplot_1.1.1               GenomicFeatures_1.50.4     
##  [79] hms_1.1.3                   KEGGREST_1.38.0            
##  [81] knitr_1.44                  pillar_1.9.0               
##  [83] GenomicRanges_1.50.2        rjson_0.2.21               
##  [85] ggsignif_0.6.4              codetools_0.2-19           
##  [87] stats4_4.2.3                fastmatch_1.1-3            
##  [89] XML_3.99-0.14               glue_1.6.2                 
##  [91] evaluate_0.20               png_0.1-8                  
##  [93] vctrs_0.6.2                 gtable_0.3.3               
##  [95] purrr_1.0.1                 cachem_1.0.7               
##  [97] xfun_0.39                   broom_1.0.4                
##  [99] restfulr_0.0.15             rstatix_0.7.2              
## [101] tibble_3.2.1                GenomicAlignments_1.34.1   
## [103] AnnotationDbi_1.60.2        memoise_2.0.1              
## [105] IRanges_2.32.0